Contacts of the helix formed by residues 74 - 79 (chain I) in PDB entry 6GYS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 74 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I TYR* 3.6 15.2 + - + +
72I ILE 3.9 1.1 - - - -
73I THR* 1.3 80.9 + - - +
75I ILE* 1.3 69.6 + - + +
76I GLY 3.7 0.2 - - - -
78I TYR* 3.3 23.5 - - - +
79I LYS* 3.3 38.3 + - - +
247I TYR* 4.1 16.7 - - - -
301I TYR 5.7 0.8 + - - -
302I LEU 4.5 3.1 + - - +
304I SER 4.4 2.0 + - - -
461I GLN* 4.5 3.8 - - - +
465I ARG* 4.6 16.1 - - - +
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I TYR* 3.4 31.8 + - + +
71I TRP* 3.4 42.0 - - + +
74I ASN* 1.3 82.4 - - + +
76I GLY* 1.3 64.4 + - - +
79I LYS* 2.9 57.5 + - + +
80I THR* 3.5 1.9 + - - -
304I SER 4.3 3.1 - - - +
305I GLY* 4.2 6.5 - - - -
306I PRO* 3.7 25.8 - - + -
548I ILE* 5.1 0.7 - - + -
552I ASN* 4.0 18.2 - - - +
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Residues in contact with GLY 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I TRP 2.8 21.6 + - - -
72I ILE* 3.0 9.8 + - - -
75I ILE* 1.3 75.8 - - - +
77I LEU* 1.3 61.1 + - - +
80I THR* 4.5 6.6 + - - -
548I ILE* 3.8 32.8 - - - +
606I ILE 3.8 10.6 - - - +
607I LEU* 4.4 8.0 - - - +
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ILE* 2.6 25.8 + - + +
73I THR* 4.7 0.4 - - - -
76I GLY* 1.3 73.9 - - - +
78I TYR* 1.3 96.3 + - + +
80I THR 5.3 0.2 - - - -
464I THR* 4.4 5.6 - - + -
503I LYS* 3.5 17.4 - - + +
506I LYS* 3.7 28.7 - - + +
507I LEU* 4.6 15.0 - - + +
510I LEU* 4.3 19.7 - - + -
606I ILE* 3.8 37.7 - - + +
607I LEU 4.7 5.2 - - - +
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Residues in contact with TYR 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I THR 3.2 28.3 - - - -
74I ASN* 3.3 12.6 + - - +
77I LEU* 1.3 103.2 - - + +
79I LYS* 1.3 61.3 + - + +
80I THR 3.3 10.2 + - - -
247I TYR* 3.3 56.4 - + + +
250I PRO* 3.5 10.6 - - - +
460I MET* 3.7 17.1 - - + +
461I GLN* 3.2 26.5 + - - -
464I THR* 2.8 24.7 + - + +
503I LYS* 3.7 37.9 - - + +
507I LEU* 4.7 1.0 - - - +
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Residues in contact with LYS 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I ASN* 3.3 31.4 + - - +
75I ILE* 2.9 39.9 + - + +
78I TYR* 1.3 74.5 - - + +
80I THR* 1.3 64.2 + - - +
81I LYS 4.0 1.8 - - - -
246I PRO 5.7 1.6 - - - +
247I TYR* 5.3 4.3 - - + -
250I PRO* 3.9 21.1 - - + -
301I TYR 4.5 1.2 + - - -
302I LEU 3.1 20.6 + - - -
303I GLN* 3.6 14.1 - - - +
304I SER 2.1 51.3 + - - +
305I GLY* 4.6 2.9 - - - -
306I PRO* 5.3 2.4 - - + +
307I ARG* 4.0 21.9 - - + +
552I ASN* 4.0 4.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il